Gene loci information

Transcript annotation

  • This transcript has been annotated as Transcription initiation factor IIB.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g6837 g6837.t6 TTS g6837.t6 19011135 19011135
chr_2 g6837 g6837.t6 isoform g6837.t6 19011283 19012928
chr_2 g6837 g6837.t6 exon g6837.t6.exon1 19011283 19012066
chr_2 g6837 g6837.t6 cds g6837.t6.CDS1 19011283 19012066
chr_2 g6837 g6837.t6 exon g6837.t6.exon2 19012596 19012650
chr_2 g6837 g6837.t6 cds g6837.t6.CDS2 19012596 19012650
chr_2 g6837 g6837.t6 exon g6837.t6.exon3 19012771 19012823
chr_2 g6837 g6837.t6 cds g6837.t6.CDS3 19012771 19012823
chr_2 g6837 g6837.t6 exon g6837.t6.exon4 19012912 19012928
chr_2 g6837 g6837.t6 cds g6837.t6.CDS4 19012912 19012928
chr_2 g6837 g6837.t6 TSS g6837.t6 19013035 19013035

Sequences

>g6837.t6 Gene=g6837 Length=909
ATGGCAAGCACTTCAAACTTTAAGGACAGAGTGGTTTGTGTACATCATCCAGATGCTCCT
TTAATTGAAGATTATCGAGCTGGTGATATGATTTGTTCGGAATGTGGATTAATAGTTGGT
GACAGTAATGAAAAAGCAGGAGTTGATCCATCTCGTGTTGGTGGACCAGAAAATCCTCTT
TTAAGTGGAGGTGATCTTTCAACAATGATTGGACCAGGAACTGGTGCTGCTTCATTCGAT
TCATTTGGATCTGCAAAATATCAAAATAGACGAACTATGAGTAGTTCTGATCGTGCTTTA
ATCACAGCATTCAAAGAAATAAGTTCTATGGCAGATCGCATCAATTTGCCTAAAACTATC
GTGGATAGAGCTAATAATTTATTCAAACAAGTACATGATGGAAAAAGTCTTAAAGGTCGT
TCAAATGATGCAAAAGCCTCCGCGTGTTTATATATTGCTTGTCGCCAAGAAGGAGTTCCT
CGTACTTTTAAAGAAATCTGTGCGATTAGTAGAGTGAGCAAGAAAGAAATTGGACGATGC
TTTAAACTGACATTAAAAGCACTTGCCACTTCTGTTGATCTCATCACAACGGCCGATTTT
ATGTCTAGATTTTGTGCAAATTTGGTACTGCCTAATTATGTTCAGCGAGCTGCAACTCAT
ATTGCGCGAAAAGCTGTTGAAATGGATATTGTTGCAGGAAGATCACCTATTTCAGTGGCT
GCTGCAGCAATTTATATGGCATCACAAGCATCTGAAAATAAAAAGACACACAAGGAAATT
GGCGATATTGCGGGTGTAGCAGAAGCAACAATTCGTCAATCGTACAAATTAATGTATGGA
CATGCAAAAGCATTATTTCCTGAAGACTTTCCATTTGCAACTCCAATTGAACAGCTTCCG
CTGTTGTAA

>g6837.t6 Gene=g6837 Length=302
MASTSNFKDRVVCVHHPDAPLIEDYRAGDMICSECGLIVGDSNEKAGVDPSRVGGPENPL
LSGGDLSTMIGPGTGAASFDSFGSAKYQNRRTMSSSDRALITAFKEISSMADRINLPKTI
VDRANNLFKQVHDGKSLKGRSNDAKASACLYIACRQEGVPRTFKEICAISRVSKKEIGRC
FKLTLKALATSVDLITTADFMSRFCANLVLPNYVQRAATHIARKAVEMDIVAGRSPISVA
AAAIYMASQASENKKTHKEIGDIAGVAEATIRQSYKLMYGHAKALFPEDFPFATPIEQLP
LL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g6837.t6 CDD cd00043 CYCLIN 100 183 1.05451E-13
18 g6837.t6 CDD cd00043 CYCLIN 194 279 8.88271E-13
17 g6837.t6 Gene3D G3DSA:2.20.25.10 - 2 44 2.8E-12
16 g6837.t6 Gene3D G3DSA:1.10.472.10 - 99 195 1.9E-40
15 g6837.t6 Gene3D G3DSA:1.10.472.10 - 196 301 1.7E-32
3 g6837.t6 PANTHER PTHR11618 TRANSCRIPTION INITIATION FACTOR IIB-RELATED 13 283 4.6E-72
4 g6837.t6 PANTHER PTHR11618:SF13 TRANSCRIPTION INITIATION FACTOR IIB 13 283 4.6E-72
8 g6837.t6 PRINTS PR00685 Transcription initiation factor IIB signature 25 45 3.4E-64
11 g6837.t6 PRINTS PR00685 Transcription initiation factor IIB signature 49 70 3.4E-64
6 g6837.t6 PRINTS PR00685 Transcription initiation factor IIB signature 147 166 3.4E-64
10 g6837.t6 PRINTS PR00685 Transcription initiation factor IIB signature 173 188 3.4E-64
5 g6837.t6 PRINTS PR00685 Transcription initiation factor IIB signature 200 218 3.4E-64
9 g6837.t6 PRINTS PR00685 Transcription initiation factor IIB signature 234 250 3.4E-64
7 g6837.t6 PRINTS PR00685 Transcription initiation factor IIB signature 266 280 3.4E-64
2 g6837.t6 Pfam PF00382 Transcription factor TFIIB repeat 107 177 2.9E-27
1 g6837.t6 Pfam PF00382 Transcription factor TFIIB repeat 201 271 5.6E-25
21 g6837.t6 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 139 154 -
20 g6837.t6 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 233 248 -
24 g6837.t6 ProSiteProfiles PS51134 Zinc finger TFIIB-type profile. 9 40 8.653
22 g6837.t6 SMART SM00385 cyclin_7 105 186 2.4E-10
23 g6837.t6 SMART SM00385 cyclin_7 199 280 1.2E-10
14 g6837.t6 SUPERFAMILY SSF57783 Zinc beta-ribbon 9 47 1.7E-7
13 g6837.t6 SUPERFAMILY SSF47954 Cyclin-like 100 190 1.34E-25
12 g6837.t6 SUPERFAMILY SSF47954 Cyclin-like 195 301 2.64E-31

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0017025 TBP-class protein binding MF
GO:0070897 transcription preinitiation complex assembly BP
GO:0006352 DNA-templated transcription, initiation BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed